Cytomegalovirus (CMV) disease is a relatively frequent, and often serious, complication in immunocompromised, CMV-infected patients. In the past few years, it has become apparent that to differentiate between subclinical viral shedding and large-scale viral replication, occurring during the prodrome before the onset of active disease, it is necessary to use sequential monitoring with a quantitative assay. Several studies have shown that CMV quantitative polymerase chain reaction (PCR) assays are more sensitive than buffy coat CMV antigen detection assays. This extra sensitivity can, in some cases, give an additional week of warning before the onset of CMV disease and allow institution of antiviral therapy at an earlier time point in the prodromal stage of CMV disease. We have developed a quantitative real-time CMV PCR assay. This assay utilizes frequency resonance energy transfer fluorescence probes and is designed to run on the Roche LightCycler. Amplification and detection of signal with this assay can be completed within 45 to 50 minutes. We have conducted a prospective study utilizing the real-time CMV PCR assay to test whole blood samples from bone marrow transplant patients. During FY 2003 analysis of the prospective study data has revealed that the real-time PCR assay has a high degree of sensitivity for detecting viremic episodes which are detected by CMV antigen and a negative predictive of greater than 95% for CMV antigen negative specimens.